K2 Variable Catalogue II: Machine Learning Classification of Variable Stars and Eclipsing Binaries in K2 Fields 0-4

We are entering an era of unprecedented quantities of data from current and planned survey telescopes. To maximise the potential of such surveys, automated data analysis techniques are required. Here we implement a new methodology for variable star classification, through the combination of Kohonen Self Organising Maps (SOM, an unsupervised machine learning algorithm) and the more common Random Forest (RF) supervised machine learning technique. We apply this method to data from the K2 mission fields 0-4, finding 154 ab-type RR Lyraes (10 newly discovered), 377 Delta Scuti pulsators, 133 Gamma Doradus pulsators, 183 detached eclipsing binaries, 290 semi-detached or contact eclipsing binaries and 9399 other periodic (mostly spot-modulated) sources, once class significance cuts are taken into account. We present lightcurve features for all K2 stellar targets, including their three strongest detected frequencies, which can be used to study stellar rotation periods where the observed variability arises from spot modulation. The resulting catalogue of variable stars, classes, and associated data features are made available online. We publish our SOM code in Python as part of the open source PyMVPA package, which in combination with already available RF modules can be easily used to recreate the method.Comment: Accepted for publication in MNRAS, 16 pages, 13 figures. Updated with proof corrections. Full catalogue tables available at https://www2.warwick.ac.uk/fac/sci/physics/research/astro/people/armstrong/ or at the CD

The object binary interface: C++ objects for evolvable shared class libraries

Object-oriented design and object-oriented languages support the development of independent software components such as class libraries. When using such components, versioning becomes a key issue. While various ad-hoc techniques and coding idioms have been used to provide versioning, all of these techniques have deficiencies - ambiguity, the necessity of recompilation or re-coding, or the loss of binary compatibility of programs. Components from different software vendors are versioned at different times. Maintaining compatibility between versions must be consciously engineered. New technologies such as distributed objects further complicate libraries by requiring multiple implementations of a type simultaneously in a program. This paper describes a new C++ object model called the Shared Object Model for C++ users and a new implementation model called the Object Binary Interface for C++ implementors. These techniques provide a mechanism for allowing multiple implementations of an object in a program. Early analysis of this approach has shown it to have performance broadly comparable to conventional implementations

Magic with Dynamo -- Flexible Cross-Component Linking for Java with Invokedynamic

Modern software systems are not built from scratch. They use functionality provided by libraries. These libraries evolve and often upgrades are deployed without the systems being recompiled. In Java, this process is particularly error-prone due to the mismatch between source and binary compatibility, and the lack of API stability in many popular libraries. We propose a novel approach to mitigate this problem based on the use of invokedynamic instructions for cross-component method invocations. The dispatch mechanism of invokedynamic is used to provide on-the-fly signature adaptation. We show how this idea can be used to construct a Java compiler that produces more resilient bytecode. We present the dynamo compiler, a proof-of-concept implemented as a javac post compiler. We evaluate our approach using several benchmark examples and two case studies showing how the dynamo compiler can prevent certain types of linkage and stack overflow errors that have been observed in real-world systems

GUASOM: An Adaptive Visualization Tool for Unsupervised Clustering in Spectrophotometric Astronomical Surveys

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] We present an adaptive visualization tool for unsupervised classification of astronomical objects in a Big Data context such as the one found in the increasingly popular large spectrophotometric sky surveys. This tool is based on an artificial intelligence technique, Kohonen’s self-organizing maps, and our goal is to facilitate the analysis work of the experts by means of oriented domain visualizations, which is impossible to achieve by using a generic tool. We designed a client-server that handles the data treatment and computational tasks to give responses as quickly as possible, and we used JavaScript Object Notation to pack the data between server and client. We optimized, parallelized, and evenly distributed the necessary calculations in a cluster of machines. By applying our clustering tool to several databases, we demonstrated the main advantages of an unsupervised approach: the classification is not based on pre-established models, thus allowing the “natural classes” present in the sample to be discovered, and it is suited to isolate atypical cases, with the important potential for discovery that this entails. Gaia Utility for the Analysis of self-organizing maps is an analysis tool that has been developed in the context of the Data Processing and Analysis Consortium, which processes and analyzes the observations made by ESA’s Gaia satellite (European Space Agency) and prepares the mission archive that is presented to the international community in sequential periodic publications. Our tool is useful not only in the context of the Gaia mission, but also allows segmenting the information present in any other massive spectroscopic or spectrophotometric database.This work made use of the infrastructures acquired with grants provided by the State Research Agency (AEI) of the Spanish Government and the European Regional Development Fund (FEDER), RTI2018-095076-B-C22. We acknowledge support from CIGUS-CITIC, funded by Xunta de Galicia and the European Union (FEDER Galicia 2014-2020 Program) through grant ED431G 2019/01 and research consolidation grant ED431B 2021/36. This work has made use of data from the European Space Agency (ESA) mission Gaia (https://www.cosmos.esa.int/gaia), processed by the Gaia Data Processing and Analysis Consortium (DPAC), https://www.cosmos.esa.int/web/gaia/dpac/consortium). Funding for the DPAC has been provided by national institutions, in particular the institutions participating in the Gaia Multilateral Agreement. Funding for the Sloan Digital Sky Survey IV has been provided by the Alfred P. Sloan Foundation, the U.S. Department of Energy Office of Science, and the Participating Institutions. SDSS-IV acknowledges support and resources from the Center for High Performance Computing at the University of Utah. The SDSS website is www.sdss.org. SDSS-IV is managed by the Astrophysical Research Consortium for the Participating Institutions of the SDSS Collaboration. We also want to acknowledge Alhambra survey funded by the Spanish Goverment under Grant AYA2006-14056. Open Access funding provided thanks to the Universidade da Coruña/CISUG agreement with Springer NatureXunta de Galicia; ED431G 2019/01Xunta de Galicia; ED431B 2021/3

Java binary computability is almost correct version 2∝

The Java language description is unusual in that it defines the effect of interleaving separate compilation and source code modifications. In Java, certain source code modifications, such as adding a method to a class, are defined as binary compatible. The Java language description does not require the re-compilation of programs importing classes or interfaces which were modified in binary compatible ways, and it claims that successful linking and execution of the altered program is guaranteed. In this paper we show that Java binary compatibility does not actually guarantee successful linking and execution. We then suggest a framework in which we formalize the requirement of safe linking and execution without re-compilation and we propose a more modest definition of binary compatibility. We prove for a substantial subset of Java, that our definition guarantees safe linking and execution

Infections Related to the Use of Medical Devices and Changes in the Oropharyngeal Flora

Background: Humans exist in mutualistic balance with a large range of microbiota. Illness and hospitalization can disturb this balance and contribute to hospital-acquired infections (HAIs), which occur most often in critically ill patients. The use of medical devices such as central venous catheters (CVCs) and endotracheal tubes (ETTs) is essential in the care of critically ill patients. At the same time, they increase the risk of HAI by forcing or disrupting the normal barriers in the human body. All such devices eventually become colonized with microbes (usually normal flora), that form biofilms on the surface of the foreign material and subsequently lead to infection. The three types of devices related to the majority of HAIs in the intensive care unit are ETTs, urinary catheters, and CVCs.Aim: The present research was conducted to study: (i) changes in oropharyngeal microbial flora during hospitalization; (ii) compare biofilm formation on widely used ETTs with different surface properties and to explore factors potentially predictive of biofilm formation; (iii) the incidence of catheter-related infections and the impact of implementing a simple hygiene insertion bundle; (iiii) compare the blood compatibility of widely used CVCs.Paper I: In a clinical observational study, oropharyngeal cultures were collected from 487 individuals: 77 controls, 193 ward patients, and 217 critically ill patients. The results indicated that occurrence of an abnormal oropharyngeal flora is an early and frequent event in hospitalized patients, particularly the critically ill. Also, colonization with gut flora in the oropharynx was common in critically ill patients. Treatment with proton pump inhibitors was associated with colonization of gut flora in the oropharynx. The result of paper I reinforces the hypothesis that proton pump inhibitor use increases the risk of pneumonia by changing the oral flora, harboring gut bacteria which then may be micro aspirated into the lungs.Paper II: In a clinical observational study, biofilm formation on three widely used ETTs was compared in critically ill patients. Biofilm formation on the tubes was found to be an early and frequent event, and high-grade biofilm formation on the ETTs was associated with development of VAP. Compared to uncoated polyvinyl chloride (PVC) ETTs, silicone-coated and noble-metal-coated PVC ETTs were independently associated with reduced high-grade biofilm formation. Methods aimed at the continuous monitoring of biofilm formation are warranted. Routines for biofilm removal need further study.Paper III: This retrospective study compared the incidence of catheter-related infections and catheter-related bloodstream infections during a 2-year period starting 1 year before and ending 1 year after the implementation of a simple hygiene insertion bundle. A total of 1,722 catheter insertions were included. The incidence of catheter-related infections and catheter-related bloodstream infections in this Scandinavian cohort was low. Thus, it seems that the implementation of a simple hygiene insertion bundle was effective in reducing catheter-related infections. The use of multiple-lumen catheters was associated with increased risk of catheter-related infections.Paper IV: In an experimental study, the blood compatibility of three coated and three uncoated CVC materials was evaluated in a modified Chandler loop model imitating the flow of blood in a vein. When in contact with blood, all the tested catheters had some impact on blood cells, contact coagulation, the complement system, or inflammatory markers, although the effects varied significantly. A polyurethane catheter coated with chlorohexidine and silver sulfadiazine showed the most unfavorable blood compatibility profile. A silicone dialysis catheter exhibited the greatest variation in the blood compatibility tests. Poor blood compatibility could cause inflammation and facilitate the development of catheter-related thrombosis in patients receiving these central venous catheters, but clinical significance has to be studied further

A flexible model for dynamic linking in Java and C#

Dynamic linking supports flexible code deployment, allowing partially linked code to link further code on the fly, as needed. Thus, end-users enjoy the advantage of automatically receiving any updates, without any need for any explicit actions on their side, such as re-compilation, or re-linking. On the down side, two executions of a program may link in different versions of code, which in some cases causes subtle errors, and may mystify end-users. Dynamic linking in Java and C# are similar: the same linking phases are involved, soundness is based on similar ideas, and executions which do not throw linking errors give the same result. They are, however, not identical: the linking phases are combined differently, and take place in different order. Consequently, linking errors may be detected at different times by Java and C# runtime systems. We develop a non-deterministic model, which describes the behaviour of both Java and C# program executions. The nondeterminism allows us to describe the design space, to distill the similarities between the two languages, and to use one proof of soundness for both. We also prove that all execution strategies are equivalent with respect to terminating executions that do not throw link errors: they give the same results

Quantification of gene expression in single cells

Studies of apparently homogeneous cell populations and single cells often give highly divergent results. Cells exhibit varying responsiveness to stimuli and gene expression and they are in many aspects stochastic and unpredictable. We have developed a method to measure gene expression quantitatively in individual cells with real-time RT-PCR. mRNA for hormones, ion channels and enzymes in pancreatic alpha- and beta-cells were quantified. The distribution of transcript levels were highly skewed and was best described by a lognormal distribution. Thus, the geometric--and not the commonly used arithmetic--mean value is the appropriate measure of average expression level. In beta-cells, insulin mRNA levels were increased in response to glucose stimulation; an effect due to an increased fraction of cells with high expression. The insulin genes Ins1 and Ins2 have similar promoter regions and were indeed co regulated within single beta-cells. Na-channels in alpha- and beta-cells display very different inactivation properties (being separated by 40 mV). We measured hormone mRNA and all Na-channel isoforms in single cells and correlated gene expression with patch-clamp recordings. Cell type-specific expression of Na-channel isoforms can partly explain the divergent inactivation. Early differentiation of human embryonic stem cells involves the transcription factors Pou5f1, Nanog and Sox2. We quantified their expression in single stem cells and observed that they are not correlated with each other. Instead Pou5f1 correlates with the transcription factors Id1 and Id3. We conclude that quantitative gene expression measurements on single cells allow: 1) studies of cell population heterogeneity and noise in gene expression; 2) exploration of genes that are co-regulated; and 3) correlation of gene expression with functional properties such as electrophysiological properties

Community health assessment using self-organizing maps and geographic information systems

<p>Abstract</p> <p>Background</p> <p>From a public health perspective, a healthier community environment correlates with fewer occurrences of chronic or infectious diseases. Our premise is that community health is a non-linear function of environmental and socioeconomic effects that are not normally distributed among communities. The objective was to integrate multivariate data sets representing social, economic, and physical environmental factors to evaluate the hypothesis that communities with similar environmental characteristics exhibit similar distributions of disease.</p> <p>Results</p> <p>The SOM algorithm used the intrinsic distributions of 92 environmental variables to classify 511 communities into five clusters. SOM determined clusters were reprojected to geographic space and compared with the distributions of several health outcomes. ANOVA results indicated that the variability between community clusters was significant with respect to the spatial distribution of disease occurrence.</p> <p>Conclusion</p> <p>Our study demonstrated a positive relationship between environmental conditions and health outcomes in communities using the SOM-GIS method to overcome data and methodological challenges traditionally encountered in public health research. Results demonstrated that community health can be classified using environmental variables and that the SOM-GIS method may be applied to multivariate environmental health studies.</p